Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion/Experiment 3
Curated date: 2021/07/01
Curator: Samara.Khan
Revision editor(s): Samara.Khan, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Brazil
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Uterus Uterus,uterus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Endometriosis endometriosis,Endometriosis (clinical),endometriosis (disease),Endometriosis (disorder),Endometriosis (morphologic abnormality),ENDOMETRIOSIS NEC,Endometriosis NOS,Endometriosis NOS (disorder),Endometriosis of other specified sites,Endometriosis, site unspecified,Endometriosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- endometriotic lesion samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- endometriotic lesion samples collected and processed for the evaluation of their bacterial profile:
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- within 30 days prior to sample collection
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 4B
Description: When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were increased: aerococcus, staphylococcus, sphingomonas, alishewanella, pseudomonas, and enterococcus
Abundance in Group 1: increased abundance in endometriotic lesion samples
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Staphylococcus | ||
| Sphingomonas | ||
| Alishewanella | ||
| Pseudomonas | ||
| Enterococcus |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 4B
Description: When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were decreased: prevotella, atopobium, afipia, mobiluncus, campylobacter, and facklamia
Abundance in Group 1: decreased abundance in endometriotic lesion samples
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Atopobium | ||
| Afipia | ||
| Mobiluncus | ||
| Campylobacter | ||
| Facklamia |
Revision editor(s): Samara.Khan
